Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:23:27 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for PhenStat on merida1


To the developers/maintainers of the PhenStat package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PhenStat.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1447/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhenStat 2.32.0  (landing page)
Hamed Haselimashhadi
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/PhenStat
git_branch: RELEASE_3_15
git_last_commit: 2e144f6
git_last_commit_date: 2022-04-26 11:17:16 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PhenStat
Version: 2.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhenStat_2.32.0.tar.gz
StartedAt: 2022-10-19 06:06:11 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 06:10:03 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 232.0 seconds
RetCode: 0
Status:   OK  
CheckDir: PhenStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhenStat_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/PhenStat.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhenStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhenStat’ version ‘2.32.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PhenStat’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘SmoothWin’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 6.131   0.05   6.534
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/PhenStat.Rcheck/00check.log’
for details.



Installation output

PhenStat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PhenStat
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘PhenStat’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PhenStat)

Tests output

PhenStat.Rcheck/tests/runTests.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("PhenStat")

 >=========================================================================<
 This version of PhenStat includes *FEWER* functions than the previous ones 
 You *still* can use the previous functions by using `:::`. For example :   
 PhenStat:::boxplotSexGenotype   or   PhenStat:::FisherExactTest            
 *** Want to know what is new in this version? run PhenStat:::WhatIsNew()   
 >=========================================================================<


RUNIT TEST PROTOCOL -- Wed Oct 19 06:09:49 2022 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
PhenStat RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  6.242   0.410   6.696 

Example timings

PhenStat.Rcheck/PhenStat-Ex.timings

nameusersystemelapsed
FisherExactTest0.3060.0350.357
JSONOutput1.6240.0351.736
LRDataset0.0990.0060.108
PhenList-class0.3010.0080.327
PhenList0.3230.0070.348
PhenStatReport0.0680.0010.072
PhenTestResult-class1.3730.0171.482
PhenTestResult1.1280.0091.210
RRTest0.1620.0020.171
TFDataset0.5750.0080.613
analysedDataset1.2630.0151.351
analysisResults1.2540.0081.324
boxplotResidualBatch1.3560.0121.419
boxplotSexGenotype0.1280.0040.142
boxplotSexGenotypeBatch0.2710.0050.293
boxplotSexGenotypeBatchAdjusted0.1240.0020.136
boxplotSexGenotypeResult1.6230.0111.743
boxplotSexGenotypeWeightBatchAdjusted0.1230.0020.133
categoricalBarplot0.5590.0090.597
checkDataset0.0660.0020.070
classificationTag1.2460.0111.333
determiningLambda1.2340.1921.512
dim0.0670.0010.073
finalLRModel0.9330.0101.002
finalModel1.0660.0031.129
finalTFModel1.0350.0321.085
htestPhenStat-class0.2440.0070.264
modelFormula0.0000.0000.001
modelFormulaLR000
parserOutputSummary1.2680.0091.330
parserOutputSummaryLR0.8690.0140.907
parserOutputTFSummary0.2120.0020.228
performReverseTransformation0.0000.0000.001
performTransformation0.0010.0000.000
plot.PhenList3.9440.0654.136
plot.PhenTestResult3.8600.0684.038
plotResidualPredicted1.2680.0061.342
printLROutput0.8460.0080.899
printTabStyle0.0020.0000.002
qqplotGenotype1.3130.0151.386
qqplotRandomEffects1.2640.0071.330
qqplotRotatedResiduals6.1310.0506.534
recommendMethod0.5200.0060.549
scatterplotGenotypeWeight0.2470.0050.267
scatterplotGenotypeWeightResult1.6530.0141.783
scatterplotSexGenotypeBatch0.1580.0040.174
scatterplotSexGenotypeBatchResult1.6380.0131.686
startLRModel0.7220.0070.732
startModel1.0440.0071.056
startTFModel0.9340.0100.947
summaryOutput1.4810.0181.504
summaryPhenListResult1.4960.0121.511
testDataset3.8150.0623.909
testFinalLRModel0.8030.0040.810
testFinalModel1.4150.0071.429
vectorOutput1.5030.0211.544
vectorOutputMatrices0.2600.0150.277